Bar Charts enable you to compare filters (gated populations) between Metadata groups or Files.
1. Add a Figure task to your workflow
Click Add new child task and select Figure from the task selector. Note that your Workflow might look slightly different, if you are using Compact View.
2. Add a Bar Chart to your Figure
Click on New Plot from either button shown above, and select Bar Chart.
3. Select the Files you want to view on the Bar Chart
Select your Bar Chart by clicking on the selector that the arrow is pointing to in the image above. Then click on Settings to view Bar Chart Settings. By default, all Files are selected. If you wish to view a subset of the files, select those using the Select Files dropdown shown above.
Most dropdowns in OMIQ allow you to filter the list, just start typing. You can even filter by metadata.
4. Select the Filters you want to compare
Select the Filters you want to compare between Files or Metadata using the Select Filters dropdown shown above.
You can easily customize the colors for your Filters using a list of hex codes. Find out how here.
5. Select the Statistic you want to display on the Y-axis
Percent of Parent is shown on the Y-axis by default. You can change this to Percent of Total, Percent of Grandparent or Count.
Hover over the Filters on your Bar Chart to view the Statistic value. To show these on the Bar Chart, click the Show Bar Values checkbox.
6. Select the Metadata you want to display on the X-axis
By default, the first Metadata that has two different categories is selected. You can change this using the Metadata dropdown shown above. Selecting None as an option will display the Files selected in Step (3) on the X-axis. In the above image, Metadata has been change to Sample Type.
If you have a lot of different categories in your selected Metadata, you may find it useful to click the Flip XY Axes checkbox, to view the Bar Chart horizontally.
7. Select the Plot Type
There are three different Bar Chart Plot Types to select from, each are described below, with examples.
In a Stacked Bar Chart, selected Filters are stacked on top of each other. This is the default selection.
In a Grouped Bar Chart, selected Filters are beside each other.
A Filled Bar Chart is a Stacked Bar Chart that has been normalized.
We suggest caution when viewing child and parent Filters together with this Plot Type as it shows normalized parts-of-the-whole. This can be misleading because the parent Filter is parts-of-the-whole with it's sibling Filters and the child Filter is parts-of-the-whole with it's sibling Filters.
8. Select the Concatenation Method to use
There are two different Concat Methods to select from, each are described below, with examples.
The Average Concat Method takes the average of the Statistic selected in Step (5), for the Files selected in Step (3). If you have selected Metadata in Step (6) then this will be calculated within the Metadata grouping.
For example, the image above is showing the Average Percent of Parent for the indicated Filters, within the indicated Metadata group. A specific example: for the n=21 Female samples, an average of 67.74% of CD56-gd- (the Parent Filter) were CD4+.
The Sum Concat Method takes the sum of the Statistic selected in Step (5), for the Files selected in Step (3). If you have selected Metadata in Step (6) then this will be calculated within the Metadata grouping.
For example, the image above is showing the Sum Count for the indicated Filters, within the indicated Metadata group. A specific example: for File: B85D75_7.fcs, there were 152, 861 CD56-gd-(Parent Filter) CD4+ cells.
To view the contribution of individual Files, click the Indicate Files checkbox. This is only possible with the Concat Method: Sum.
To move your fcs plots, advanced analysis plots and Bar Charts around the Figure layout, try Canvas Mode.